Starting phenix.real_space_refine on Mon May 12 15:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7s_44322/05_2025/9b7s_44322.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5799 2.51 5 N 1638 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9273 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 964 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 8 Chain: "B" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 521 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "C" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2258 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265} Chain breaks: 5 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain breaks: 8 Chain: "E" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 521 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "F" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2258 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265} Chain breaks: 5 Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Time building chain proxies: 5.58, per 1000 atoms: 0.60 Number of scatterers: 9273 At special positions: 0 Unit cell: (128.148, 97.016, 82.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1805 8.00 N 1638 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 7.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.580A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.214A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.833A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.054A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.762A pdb=" N PHE D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.010A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.908A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 564 through 569 removed outlier: 4.149A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.877A pdb=" N THR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 517 removed outlier: 4.135A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 451 removed outlier: 6.686A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 450 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.847A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 305 through 307 removed outlier: 3.507A pdb=" N GLY C 307 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.422A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.751A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 479 through 480 removed outlier: 6.156A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AB2, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AB3, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AB4, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AB5, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AB6, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.011A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 445 through 451 removed outlier: 6.707A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR E 450 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 593 through 596 removed outlier: 3.972A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 305 through 307 removed outlier: 6.392A pdb=" N GLN F 688 " --> pdb=" O TRP F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.387A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 445 through 451 removed outlier: 5.775A pdb=" N LEU F 447 " --> pdb=" O SER F 464 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER F 464 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS F 449 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE F 451 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR F 460 " --> pdb=" O ILE F 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 479 through 480 removed outlier: 6.430A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AC5, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AC7, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC8, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.825A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 26 through 28 removed outlier: 5.576A pdb=" N THR L 91 " --> pdb=" O ALA L 47 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N HIS L 49 " --> pdb=" O SER L 89 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N SER L 89 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N VAL L 51 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N SER L 87 " --> pdb=" O VAL L 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 32 through 35 removed outlier: 6.315A pdb=" N LEU L 33 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP L 57 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 32 through 35 removed outlier: 6.315A pdb=" N LEU L 33 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR L 118 " --> pdb=" O GLN L 112 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2429 1.33 - 1.45: 2039 1.45 - 1.57: 4978 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 9498 Sorted by residual: bond pdb=" C GLU F 723 " pdb=" O GLU F 723 " ideal model delta sigma weight residual 1.246 1.224 0.023 9.20e-03 1.18e+04 6.02e+00 bond pdb=" C PRO C 365 " pdb=" O PRO C 365 " ideal model delta sigma weight residual 1.246 1.225 0.021 8.50e-03 1.38e+04 5.93e+00 bond pdb=" CG GLN L 112 " pdb=" CD GLN L 112 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.57e+00 bond pdb=" CA TYR H 127 " pdb=" C TYR H 127 " ideal model delta sigma weight residual 1.522 1.498 0.025 1.20e-02 6.94e+03 4.20e+00 bond pdb=" C ALA H 129 " pdb=" O ALA H 129 " ideal model delta sigma weight residual 1.234 1.208 0.026 1.27e-02 6.20e+03 4.12e+00 ... (remaining 9493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12163 1.90 - 3.80: 596 3.80 - 5.70: 85 5.70 - 7.60: 14 7.60 - 9.50: 7 Bond angle restraints: 12865 Sorted by residual: angle pdb=" N GLY F 539 " pdb=" CA GLY F 539 " pdb=" C GLY F 539 " ideal model delta sigma weight residual 112.77 121.75 -8.98 1.28e+00 6.10e-01 4.92e+01 angle pdb=" C GLY H 28 " pdb=" N GLY H 29 " pdb=" CA GLY H 29 " ideal model delta sigma weight residual 122.16 117.73 4.43 7.70e-01 1.69e+00 3.31e+01 angle pdb=" N ASN H 50 " pdb=" CA ASN H 50 " pdb=" C ASN H 50 " ideal model delta sigma weight residual 111.28 117.23 -5.95 1.09e+00 8.42e-01 2.98e+01 angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 112.73 119.16 -6.43 1.20e+00 6.94e-01 2.87e+01 angle pdb=" N VAL L 117 " pdb=" CA VAL L 117 " pdb=" C VAL L 117 " ideal model delta sigma weight residual 109.30 116.26 -6.96 1.31e+00 5.83e-01 2.82e+01 ... (remaining 12860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5260 17.74 - 35.48: 201 35.48 - 53.21: 35 53.21 - 70.95: 11 70.95 - 88.69: 13 Dihedral angle restraints: 5520 sinusoidal: 2166 harmonic: 3354 Sorted by residual: dihedral pdb=" CA THR C 729 " pdb=" C THR C 729 " pdb=" N ARG C 730 " pdb=" CA ARG C 730 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER L 74 " pdb=" C SER L 74 " pdb=" N THR L 75 " pdb=" CA THR L 75 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN F 519 " pdb=" C ASN F 519 " pdb=" N PRO F 520 " pdb=" CA PRO F 520 " ideal model delta harmonic sigma weight residual 0.00 -21.86 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 970 0.061 - 0.122: 272 0.122 - 0.183: 44 0.183 - 0.244: 18 0.244 - 0.306: 5 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CA ILE L 114 " pdb=" N ILE L 114 " pdb=" C ILE L 114 " pdb=" CB ILE L 114 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR L 113 " pdb=" N TYR L 113 " pdb=" C TYR L 113 " pdb=" CB TYR L 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR A 484 " pdb=" N TYR A 484 " pdb=" C TYR A 484 " pdb=" CB TYR A 484 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1306 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 495 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLN F 495 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN F 495 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN F 496 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 129 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ALA H 129 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA H 129 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY H 130 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 138 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP H 138 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 138 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 138 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 138 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 138 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 138 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 138 " -0.000 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 135 2.64 - 3.21: 8283 3.21 - 3.77: 13958 3.77 - 4.34: 20572 4.34 - 4.90: 33355 Nonbonded interactions: 76303 Sorted by model distance: nonbonded pdb=" O ASN F 498 " pdb=" ND2 ASN F 498 " model vdw 2.076 3.120 nonbonded pdb=" NH2 ARG C 296 " pdb=" OE1 GLU F 690 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR D 279 " pdb=" O TYR D 377 " model vdw 2.233 3.040 nonbonded pdb=" O SER H 125 " pdb=" OG SER H 125 " model vdw 2.243 3.040 nonbonded pdb=" O GLN C 442 " pdb=" N LEU C 444 " model vdw 2.247 3.120 ... (remaining 76298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 252 through 601 or resid 623 through 670)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9500 Z= 0.388 Angle : 0.961 9.500 12869 Z= 0.599 Chirality : 0.062 0.306 1309 Planarity : 0.005 0.038 1702 Dihedral : 11.275 88.689 3376 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.11 % Allowed : 2.83 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1111 helix: -1.86 (0.69), residues: 38 sheet: -0.93 (0.33), residues: 181 loop : -1.13 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 138 HIS 0.014 0.003 HIS C 290 PHE 0.030 0.003 PHE F 367 TYR 0.027 0.003 TYR A 399 ARG 0.013 0.002 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.21485 ( 156) hydrogen bonds : angle 9.56990 ( 354) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.07977 ( 4) covalent geometry : bond 0.00810 ( 9498) covalent geometry : angle 0.96138 (12865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 1.197 Fit side-chains REVERT: C 300 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7243 (tmt90) REVERT: C 462 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7237 (tptt) REVERT: C 725 ARG cc_start: 0.8626 (ptt180) cc_final: 0.8274 (ptp-110) REVERT: F 300 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7005 (ptt180) REVERT: F 462 LYS cc_start: 0.8649 (mmtt) cc_final: 0.7228 (tmtm) REVERT: F 514 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7091 (mmt180) REVERT: F 689 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8466 (mttt) REVERT: H 24 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (tt) REVERT: H 31 VAL cc_start: 0.9063 (m) cc_final: 0.8792 (p) outliers start: 11 outliers final: 2 residues processed: 198 average time/residue: 1.1275 time to fit residues: 239.7913 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 94 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN C 360 HIS ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 700 GLN C 709 ASN D 259 GLN D 387 GLN D 519 ASN D 624 HIS E 452 ASN E 585 GLN F 360 HIS F 452 ASN F 470 ASN F 495 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 ASN F 562 ASN F 608 GLN F 700 GLN F 709 ASN H 96 ASN L 59 GLN L 101 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.079567 restraints weight = 18956.469| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.03 r_work: 0.2934 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9500 Z= 0.153 Angle : 0.572 6.724 12869 Z= 0.306 Chirality : 0.043 0.140 1309 Planarity : 0.004 0.034 1702 Dihedral : 5.335 31.359 1271 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.12 % Allowed : 8.38 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1111 helix: -0.69 (0.88), residues: 32 sheet: -0.27 (0.35), residues: 180 loop : -0.78 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.006 0.001 HIS C 290 PHE 0.016 0.002 PHE F 367 TYR 0.018 0.002 TYR C 484 ARG 0.006 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 156) hydrogen bonds : angle 6.63325 ( 354) SS BOND : bond 0.00552 ( 2) SS BOND : angle 0.85654 ( 4) covalent geometry : bond 0.00355 ( 9498) covalent geometry : angle 0.57218 (12865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.100 Fit side-chains REVERT: C 300 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7235 (ttt180) REVERT: C 462 LYS cc_start: 0.8065 (mmtt) cc_final: 0.6759 (tptt) REVERT: C 725 ARG cc_start: 0.8748 (ptt180) cc_final: 0.8142 (ptp-110) REVERT: D 485 ARG cc_start: 0.7542 (ttm170) cc_final: 0.5338 (ttt180) REVERT: E 470 ASN cc_start: 0.7936 (t0) cc_final: 0.7587 (t0) REVERT: F 300 ARG cc_start: 0.8417 (mtt180) cc_final: 0.6919 (ptt180) REVERT: F 462 LYS cc_start: 0.8586 (mmtt) cc_final: 0.6976 (tmtm) REVERT: F 514 ARG cc_start: 0.8548 (mtm180) cc_final: 0.7000 (mmt180) REVERT: F 689 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8394 (mttt) REVERT: H 31 VAL cc_start: 0.9107 (m) cc_final: 0.8766 (p) REVERT: H 62 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7948 (mmtp) REVERT: H 78 ASP cc_start: 0.8797 (m-30) cc_final: 0.8570 (m-30) REVERT: H 110 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8929 (t) REVERT: L 67 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8183 (ptt90) REVERT: L 118 THR cc_start: 0.9346 (m) cc_final: 0.9104 (p) outliers start: 21 outliers final: 8 residues processed: 165 average time/residue: 1.0548 time to fit residues: 187.6181 Evaluate side-chains 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 109 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B 585 GLN C 497 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN F 470 ASN F 497 ASN F 585 GLN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 96 ASN L 59 GLN L 64 GLN L 101 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078058 restraints weight = 19283.365| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.00 r_work: 0.2895 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9500 Z= 0.208 Angle : 0.581 9.620 12869 Z= 0.307 Chirality : 0.044 0.141 1309 Planarity : 0.004 0.041 1702 Dihedral : 5.152 31.992 1268 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.53 % Allowed : 9.09 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1111 helix: 1.96 (1.14), residues: 20 sheet: -0.29 (0.38), residues: 165 loop : -0.65 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 138 HIS 0.010 0.002 HIS C 290 PHE 0.015 0.002 PHE F 367 TYR 0.017 0.002 TYR L 113 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 156) hydrogen bonds : angle 6.24257 ( 354) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.01936 ( 4) covalent geometry : bond 0.00486 ( 9498) covalent geometry : angle 0.58120 (12865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.032 Fit side-chains REVERT: B 440 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6760 (mm) REVERT: B 575 GLU cc_start: 0.3483 (OUTLIER) cc_final: 0.2753 (pm20) REVERT: C 300 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7061 (tmm160) REVERT: C 462 LYS cc_start: 0.8066 (mmtt) cc_final: 0.6753 (tptt) REVERT: D 398 GLU cc_start: 0.8383 (mp0) cc_final: 0.7951 (mp0) REVERT: D 485 ARG cc_start: 0.7402 (ttm170) cc_final: 0.5558 (ttt90) REVERT: F 300 ARG cc_start: 0.8430 (mtt180) cc_final: 0.6886 (ptt180) REVERT: F 462 LYS cc_start: 0.8582 (mmtt) cc_final: 0.6971 (tmtm) REVERT: F 689 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8401 (mttt) REVERT: H 31 VAL cc_start: 0.9119 (m) cc_final: 0.8849 (p) REVERT: H 37 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (pt) REVERT: H 62 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8283 (mmtp) REVERT: H 78 ASP cc_start: 0.8812 (m-30) cc_final: 0.8582 (m-30) REVERT: H 86 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.6896 (mtp85) REVERT: H 110 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8887 (t) REVERT: L 67 ARG cc_start: 0.8479 (ptm-80) cc_final: 0.8206 (ptt90) REVERT: L 118 THR cc_start: 0.9339 (m) cc_final: 0.9055 (p) outliers start: 25 outliers final: 13 residues processed: 145 average time/residue: 1.1064 time to fit residues: 173.1883 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 80 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS B 452 ASN C 608 GLN F 470 ASN F 585 GLN F 588 GLN L 64 GLN L 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078716 restraints weight = 19049.201| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.03 r_work: 0.2915 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9500 Z= 0.142 Angle : 0.525 9.438 12869 Z= 0.274 Chirality : 0.042 0.137 1309 Planarity : 0.004 0.031 1702 Dihedral : 4.829 31.355 1268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.22 % Allowed : 9.90 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1111 helix: 2.51 (1.10), residues: 20 sheet: -0.05 (0.38), residues: 159 loop : -0.51 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 PHE 0.012 0.001 PHE F 367 TYR 0.013 0.001 TYR L 113 ARG 0.004 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02817 ( 156) hydrogen bonds : angle 5.88763 ( 354) SS BOND : bond 0.00528 ( 2) SS BOND : angle 0.82622 ( 4) covalent geometry : bond 0.00329 ( 9498) covalent geometry : angle 0.52488 (12865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.051 Fit side-chains REVERT: C 300 ARG cc_start: 0.8430 (ttm110) cc_final: 0.7088 (tmm160) REVERT: C 462 LYS cc_start: 0.8101 (mmtt) cc_final: 0.6765 (tptt) REVERT: D 398 GLU cc_start: 0.8303 (mp0) cc_final: 0.7720 (tm-30) REVERT: D 485 ARG cc_start: 0.7398 (ttm170) cc_final: 0.5505 (ttt90) REVERT: F 300 ARG cc_start: 0.8324 (mtt180) cc_final: 0.6904 (ptt180) REVERT: F 462 LYS cc_start: 0.8574 (mmtt) cc_final: 0.6953 (tmtm) REVERT: F 689 LYS cc_start: 0.8818 (mmtm) cc_final: 0.8398 (mttt) REVERT: H 31 VAL cc_start: 0.9131 (m) cc_final: 0.8880 (p) REVERT: H 37 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8476 (pt) REVERT: H 62 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8381 (mmtp) REVERT: H 78 ASP cc_start: 0.8791 (m-30) cc_final: 0.8578 (m-30) REVERT: H 110 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8900 (t) REVERT: L 67 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8209 (ptt90) REVERT: L 118 THR cc_start: 0.9301 (m) cc_final: 0.8991 (p) outliers start: 22 outliers final: 10 residues processed: 145 average time/residue: 1.1222 time to fit residues: 174.9685 Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN C 430 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN F 585 GLN L 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.077512 restraints weight = 19204.515| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.02 r_work: 0.2887 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9500 Z= 0.214 Angle : 0.569 9.624 12869 Z= 0.299 Chirality : 0.044 0.142 1309 Planarity : 0.004 0.037 1702 Dihedral : 4.969 32.543 1268 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.03 % Allowed : 10.40 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1111 helix: 2.60 (1.09), residues: 20 sheet: -0.19 (0.39), residues: 161 loop : -0.57 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 509 HIS 0.008 0.001 HIS F 290 PHE 0.012 0.002 PHE F 367 TYR 0.015 0.002 TYR L 113 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 156) hydrogen bonds : angle 5.95696 ( 354) SS BOND : bond 0.00579 ( 2) SS BOND : angle 0.84169 ( 4) covalent geometry : bond 0.00499 ( 9498) covalent geometry : angle 0.56871 (12865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.987 Fit side-chains REVERT: B 575 GLU cc_start: 0.3394 (OUTLIER) cc_final: 0.2592 (pm20) REVERT: C 300 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7048 (tmm160) REVERT: C 462 LYS cc_start: 0.8089 (mmtt) cc_final: 0.6702 (tptm) REVERT: D 398 GLU cc_start: 0.8365 (mp0) cc_final: 0.7782 (tm-30) REVERT: D 485 ARG cc_start: 0.7396 (ttm170) cc_final: 0.5593 (ttt90) REVERT: F 462 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7400 (mmmt) REVERT: F 689 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8363 (mttt) REVERT: H 31 VAL cc_start: 0.9130 (m) cc_final: 0.8898 (p) REVERT: H 37 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8482 (pt) REVERT: H 62 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8387 (mmtp) REVERT: H 78 ASP cc_start: 0.8786 (m-30) cc_final: 0.8578 (m-30) REVERT: L 52 SER cc_start: 0.8473 (t) cc_final: 0.8098 (p) REVERT: L 67 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.8216 (ptt90) REVERT: L 118 THR cc_start: 0.9326 (m) cc_final: 0.9031 (p) outliers start: 30 outliers final: 13 residues processed: 146 average time/residue: 1.0907 time to fit residues: 171.4324 Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 67 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 overall best weight: 2.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN F 585 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079268 restraints weight = 18939.406| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.01 r_work: 0.2922 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9500 Z= 0.118 Angle : 0.501 8.811 12869 Z= 0.260 Chirality : 0.041 0.133 1309 Planarity : 0.003 0.030 1702 Dihedral : 4.599 31.588 1268 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.42 % Allowed : 11.52 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1111 helix: 2.97 (1.14), residues: 20 sheet: 0.06 (0.39), residues: 162 loop : -0.49 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 509 HIS 0.004 0.001 HIS C 290 PHE 0.009 0.001 PHE F 367 TYR 0.012 0.001 TYR L 113 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 156) hydrogen bonds : angle 5.66746 ( 354) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.83405 ( 4) covalent geometry : bond 0.00274 ( 9498) covalent geometry : angle 0.50092 (12865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.121 Fit side-chains REVERT: B 575 GLU cc_start: 0.3401 (OUTLIER) cc_final: 0.2647 (pm20) REVERT: C 300 ARG cc_start: 0.8432 (ttm110) cc_final: 0.7064 (tmm160) REVERT: C 462 LYS cc_start: 0.8084 (mmtt) cc_final: 0.6727 (tptt) REVERT: D 398 GLU cc_start: 0.8254 (mp0) cc_final: 0.7705 (tm-30) REVERT: D 485 ARG cc_start: 0.7360 (ttm170) cc_final: 0.5434 (ttt180) REVERT: F 462 LYS cc_start: 0.8550 (mmtt) cc_final: 0.7424 (mmmt) REVERT: F 689 LYS cc_start: 0.8774 (mmtm) cc_final: 0.8329 (mttt) REVERT: H 37 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8397 (pt) REVERT: H 62 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8394 (mmtm) REVERT: H 78 ASP cc_start: 0.8779 (m-30) cc_final: 0.8548 (m-30) REVERT: H 92 ASP cc_start: 0.8572 (t0) cc_final: 0.8266 (t0) REVERT: L 67 ARG cc_start: 0.8443 (ptm-80) cc_final: 0.8210 (ptt90) REVERT: L 118 THR cc_start: 0.9302 (m) cc_final: 0.8930 (p) outliers start: 24 outliers final: 13 residues processed: 138 average time/residue: 1.1428 time to fit residues: 169.8602 Evaluate side-chains 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.077101 restraints weight = 19280.440| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.02 r_work: 0.2874 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9500 Z= 0.233 Angle : 0.572 7.899 12869 Z= 0.301 Chirality : 0.044 0.142 1309 Planarity : 0.004 0.036 1702 Dihedral : 4.962 33.353 1268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.32 % Allowed : 12.22 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1111 helix: 2.70 (1.10), residues: 20 sheet: -0.12 (0.40), residues: 161 loop : -0.57 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 509 HIS 0.008 0.001 HIS F 290 PHE 0.011 0.002 PHE F 367 TYR 0.016 0.002 TYR L 113 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 156) hydrogen bonds : angle 5.93120 ( 354) SS BOND : bond 0.00603 ( 2) SS BOND : angle 0.80011 ( 4) covalent geometry : bond 0.00545 ( 9498) covalent geometry : angle 0.57221 (12865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.076 Fit side-chains REVERT: B 575 GLU cc_start: 0.3300 (OUTLIER) cc_final: 0.2557 (pm20) REVERT: C 300 ARG cc_start: 0.8489 (ttm110) cc_final: 0.7048 (tmm160) REVERT: C 462 LYS cc_start: 0.8131 (mmtt) cc_final: 0.6695 (tptt) REVERT: D 398 GLU cc_start: 0.8355 (mp0) cc_final: 0.7774 (tm-30) REVERT: D 485 ARG cc_start: 0.7476 (ttm170) cc_final: 0.5482 (ttt180) REVERT: F 462 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7366 (mmmt) REVERT: F 689 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8322 (mttt) REVERT: H 37 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8464 (pt) REVERT: H 62 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8518 (mmtm) REVERT: H 78 ASP cc_start: 0.8813 (m-30) cc_final: 0.8593 (m-30) REVERT: H 86 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6911 (mtp85) REVERT: H 92 ASP cc_start: 0.8615 (t0) cc_final: 0.8315 (t0) REVERT: L 52 SER cc_start: 0.8609 (t) cc_final: 0.8232 (p) REVERT: L 67 ARG cc_start: 0.8482 (ptm-80) cc_final: 0.8221 (ptt90) outliers start: 23 outliers final: 15 residues processed: 133 average time/residue: 1.1491 time to fit residues: 164.4666 Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain F residue 585 GLN Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN F 588 GLN L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.080505 restraints weight = 19248.772| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.07 r_work: 0.2943 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9500 Z= 0.082 Angle : 0.486 8.918 12869 Z= 0.248 Chirality : 0.040 0.229 1309 Planarity : 0.003 0.030 1702 Dihedral : 4.359 30.756 1268 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.52 % Allowed : 12.83 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1111 helix: 3.09 (1.17), residues: 20 sheet: 0.23 (0.40), residues: 162 loop : -0.45 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 116 HIS 0.003 0.000 HIS C 290 PHE 0.008 0.001 PHE C 535 TYR 0.009 0.001 TYR L 113 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02245 ( 156) hydrogen bonds : angle 5.43734 ( 354) SS BOND : bond 0.00459 ( 2) SS BOND : angle 0.52417 ( 4) covalent geometry : bond 0.00187 ( 9498) covalent geometry : angle 0.48565 (12865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.127 Fit side-chains REVERT: B 441 ASP cc_start: 0.8183 (m-30) cc_final: 0.7942 (m-30) REVERT: C 300 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7045 (tmm160) REVERT: C 462 LYS cc_start: 0.8112 (mmtt) cc_final: 0.6717 (tptt) REVERT: D 398 GLU cc_start: 0.8173 (mp0) cc_final: 0.7681 (tm-30) REVERT: D 485 ARG cc_start: 0.7308 (ttm170) cc_final: 0.5583 (ttt180) REVERT: F 462 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7418 (mmmt) REVERT: F 689 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8270 (mttt) REVERT: H 37 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8261 (pt) REVERT: H 62 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8313 (mmtm) REVERT: H 92 ASP cc_start: 0.8557 (t0) cc_final: 0.8218 (t0) REVERT: L 67 ARG cc_start: 0.8428 (ptm-80) cc_final: 0.8214 (ptt90) outliers start: 15 outliers final: 7 residues processed: 142 average time/residue: 1.1600 time to fit residues: 177.3639 Evaluate side-chains 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 ASN F 470 ASN F 585 GLN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN L 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078113 restraints weight = 19049.377| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.02 r_work: 0.2893 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9500 Z= 0.181 Angle : 0.537 8.204 12869 Z= 0.279 Chirality : 0.043 0.213 1309 Planarity : 0.004 0.033 1702 Dihedral : 4.633 32.450 1268 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.11 % Allowed : 13.94 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1111 helix: 2.92 (1.12), residues: 20 sheet: 0.21 (0.39), residues: 163 loop : -0.48 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.007 0.001 HIS F 290 PHE 0.010 0.001 PHE F 367 TYR 0.015 0.002 TYR L 113 ARG 0.006 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02810 ( 156) hydrogen bonds : angle 5.64315 ( 354) SS BOND : bond 0.00575 ( 2) SS BOND : angle 0.82304 ( 4) covalent geometry : bond 0.00426 ( 9498) covalent geometry : angle 0.53666 (12865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.071 Fit side-chains REVERT: C 300 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7021 (tmm160) REVERT: C 462 LYS cc_start: 0.8120 (mmtt) cc_final: 0.6692 (tptt) REVERT: D 398 GLU cc_start: 0.8274 (mp0) cc_final: 0.7742 (tm-30) REVERT: D 485 ARG cc_start: 0.7352 (ttm170) cc_final: 0.5412 (ttt180) REVERT: F 462 LYS cc_start: 0.8520 (mmtt) cc_final: 0.7367 (mmmt) REVERT: F 689 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8279 (mttt) REVERT: H 37 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8238 (pt) REVERT: H 62 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8414 (mmtm) REVERT: H 92 ASP cc_start: 0.8584 (t0) cc_final: 0.8254 (t0) REVERT: L 67 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.8227 (ptt90) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 1.0878 time to fit residues: 147.6988 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain F residue 585 GLN Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN F 585 GLN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.090415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.080762 restraints weight = 19108.045| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.04 r_work: 0.2946 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9500 Z= 0.082 Angle : 0.484 8.079 12869 Z= 0.247 Chirality : 0.040 0.194 1309 Planarity : 0.003 0.035 1702 Dihedral : 4.279 30.612 1268 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.81 % Allowed : 14.24 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1111 helix: 3.18 (1.17), residues: 20 sheet: 0.40 (0.40), residues: 162 loop : -0.40 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 116 HIS 0.002 0.000 HIS C 290 PHE 0.007 0.001 PHE C 535 TYR 0.010 0.001 TYR F 484 ARG 0.006 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02274 ( 156) hydrogen bonds : angle 5.32385 ( 354) SS BOND : bond 0.00389 ( 2) SS BOND : angle 0.60993 ( 4) covalent geometry : bond 0.00181 ( 9498) covalent geometry : angle 0.48387 (12865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: C 300 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7201 (ttp-170) REVERT: C 462 LYS cc_start: 0.8041 (mmtt) cc_final: 0.6722 (tptm) REVERT: D 398 GLU cc_start: 0.8178 (mp0) cc_final: 0.7480 (tp30) REVERT: D 485 ARG cc_start: 0.7296 (ttm170) cc_final: 0.5587 (ttt180) REVERT: F 462 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7398 (mmmt) REVERT: F 689 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8251 (mttt) REVERT: H 37 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8124 (pt) REVERT: H 62 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8331 (mmtm) REVERT: H 92 ASP cc_start: 0.8555 (t0) cc_final: 0.8206 (t0) REVERT: L 67 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.8201 (ptt90) outliers start: 8 outliers final: 8 residues processed: 130 average time/residue: 1.0947 time to fit residues: 153.4774 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain F residue 585 GLN Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN F 585 GLN F 588 GLN H 32 GLN L 64 GLN L 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.077167 restraints weight = 19163.338| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.04 r_work: 0.2875 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9500 Z= 0.243 Angle : 0.593 8.577 12869 Z= 0.309 Chirality : 0.045 0.214 1309 Planarity : 0.004 0.039 1702 Dihedral : 4.808 33.352 1268 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.41 % Allowed : 14.34 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1111 helix: 2.70 (1.10), residues: 20 sheet: 0.09 (0.40), residues: 160 loop : -0.48 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 509 HIS 0.008 0.001 HIS C 290 PHE 0.011 0.002 PHE F 367 TYR 0.017 0.002 TYR L 113 ARG 0.011 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 156) hydrogen bonds : angle 5.77531 ( 354) SS BOND : bond 0.00691 ( 2) SS BOND : angle 0.71692 ( 4) covalent geometry : bond 0.00571 ( 9498) covalent geometry : angle 0.59283 (12865) =============================================================================== Job complete usr+sys time: 5959.59 seconds wall clock time: 103 minutes 57.04 seconds (6237.04 seconds total)